GBE Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda Dong Zhang1,2,3,†,HongZou1,2,†, Cong-Jie Hua1,2,Wen-XiangLi1,2, Shahid Mahboob4,5, Khalid Abdullah Al-Ghanim4, Fahad Al-Misned4,IvanJakovlic6,*, and Gui-Tang Wang1,2,* 1Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China 2State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China 3University of Chinese Academy of Sciences, Beijing, P.R. China 4Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia 5Department of Zoology, GC University, Faisalabad, Pakistan 6Bio-Transduction Lab, Wuhan, P.R. China †These authors contributed equally to this work. *Corresponding authors: E-mails:
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[email protected]. Accepted: June 8, 2019 Data deposition: This project has been deposited at GenBank under the accession numbers MK079664, MK542856, MK542857 and MK542858. The remaining data are included within the article and its supplementary files. Abstract The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phy- logenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies.